1. Biomax Informatics AG Bioinformatics designed with you in mind. FunCat TM, a controlled vocabulary encompassing the biology of prokaryotes, plants and animals from cellular to systemic level Dr. Dieter Maier Manchester Ontologies Workshop 23/24.3.02 Biomax Informatics AG, Lochhamer Str. 11, 82152 Martinsried, Germany

2. Biomax Informatics AG Bioinformatics designed with you in mind. Outline Objectives Structure Content Development Use

3. Biomax Informatics AG Bioinformatics designed with you in mind. Objectives Automatic data management No prior knowledge of vocabulary required Group genes by functional categories Extensible Organism independent Compatible to other ontologies

4. Biomax Informatics AG Bioinformatics designed with you in mind. Disclaimer what the FunCat is not: - Tool for the complete description of functions on a single gene level

5. Biomax Informatics AG Bioinformatics designed with you in mind. Structure Organized hierarchicall Related functions grouped on different levels Internally consistent => => Provides a data warehouse - overview about available selection - progress from general to specific - infere from specific to general

6. Biomax Informatics AG Bioinformatics designed with you in mind. Hierarchical structure 5´-end processing rRNA-processing tRNA-transcription rRNA-transcription mRNA-transcription mRNA-processingTranscription

7. Biomax Informatics AG Bioinformatics designed with you in mind. Content Covers cellular processes, systemic physiology, development and anatomy from procaryotes to the human 25 main Categories with ~ 1500 sub-categories Categories are independent of organism Genes can belong to multiple categories

8. Biomax Informatics AG Bioinformatics designed with you in mind. Metabolism: 247 Energy: 60 Cell cycle and DNA processing: 54 Transcription: 31 Protein synthesis (Translation): 11 Protein fate (folding, modification, destination): 25 Cellular transport: 32 Cellular communication: 47 Cell rescue, defense and virulence: 50 Regulation / interaction with cellular environment: 45 Cell fate: 54 Systemic regulation / interaction with environment : 89 Development (systemic): 51 Transposable Elements, viral and plasmid proteins: 8 Control of cellular organisation: 57 Cell type differentiation: 69 Tissue differentiation: 40 Organ differentiation: 91 Enzymatic activity => EC ~ 4400 Protein activity regulation: 23 Protein with binding function / cofactor requirement: 49 Transport facilitation: 49 Molecular function: 122 Biological process: 1061 Subcellular localisation: 63 Cell type localisation: 69 Tissue localisation: 41 Organ localisation: 91 Localisation: 256

9. Biomax Informatics AG Bioinformatics designed with you in mind. Development Historical Pathways Thesaurus Complex relations

10. Biomax Informatics AG Bioinformatics designed with you in mind. Structural development Proven flexibility – easy to extend Stable overall structure Compatibel to other ontologies like - Enzyme Cataloge - Gene Ontology - EcoCyce

11. Biomax Informatics AG Bioinformatics designed with you in mind. Development in numbers S. cerevisiae 1996 Main categories: 16 Depth: 4 Total: 182 Plant (A. thaliana) and Procaryotes 1998 20 6 528 Animals (Human) 2001 25 6 1448

12. Biomax Informatics AG Bioinformatics designed with you in mind. Integrating Pathways into processes - hierachical structure allows: - Univocal attribution - Test for completeness - Test for consistence

13. Biomax Informatics AG Bioinformatics designed with you in mind. Integrating additional information Create a dynamic ontology from existing ontologies, keywords and linguistic extraction of descriptors from the literature Semiautomatic mapping of dynamic ontologie to FunCat

14. Biomax Informatics AG Bioinformatics designed with you in mind. Enabling complex relations Intensify multidimensionality Enable if... then... relations

15. Biomax Informatics AG Bioinformatics designed with you in mind. Use Manual annotation Automatic annotation Data mining

16. Biomax Informatics AG Bioinformatics designed with you in mind. Manual annotation - multidimensional - stepwise Four dimensions

17. Biomax Informatics AG Bioinformatics designed with you in mind. Manual annotation 17 manually annotated genomes (5 eucaryotes, 12 procaryotes) H.sapiens, A.thaliana, S.cerevisiae, N.crassa, propriatary: A.niger B.subtilis, T.acidophilum, Listeria, 6 public procaryotes in progress, propriatary: C.glutamicum, C.pneumoniae, 1 undisclosed Used for annotation of Transcriptomes

18. Biomax Informatics AG Bioinformatics designed with you in mind. Automatic Annotation Sequence similarity to manually annotated proteins (distinguish experimentally verified and similarity associated function): -H. sapiens -A. thaliana -S. cerevisiae -B. subtilis -T. acidophilum

19. Biomax Informatics AG Bioinformatics designed with you in mind. PEDANT Genome Database Currently more than 170 genomes (600 000 ORFs) Bacteria Archea Eucarya Thermotogales Flavobacteria Cyanobacteria Proteobacteria Gram positives Green non-sulfur bacteria Pyrodictium Thermoproteus Methanococcus Methanobacterium Methanosarcina Extreme halophiles Entamoeba Slime molds Animals Fungi Plants Ciliates Flagellates Trichomonades Microsporida Diplomonades

20. Biomax Informatics AG Bioinformatics designed with you in mind. Data mining Retrieval Visualisation Mining Integration

21. Biomax Informatics AG Bioinformatics designed with you in mind. Queries using the FunCat: Grouplevel - Looking for groups of genes:

22. Biomax Informatics AG Bioinformatics designed with you in mind. Single molecule level - Retrieving protein entries:

23. Biomax Informatics AG Bioinformatics designed with you in mind. The human FunCat Unclassified Metabolism Energy cell cycle Transcription Translation Protein fate Intracellular Transport Defense Signalling Cell physiology

24. Biomax Informatics AG Bioinformatics designed with you in mind. Comparing genomes Sequence similairty  „ functional homology“ Identification of organism specific functions

25. Biomax Informatics AG Bioinformatics designed with you in mind. Comparing H.sapiens – B.subtilis Metabolism Protein fate Cellular communication Interaction with cellular environment

26. Biomax Informatics AG Bioinformatics designed with you in mind. Integrative analysis Gene expression data Functional catalogue Functional catalogue Functional catalogue Functional catalogue Protein-protein interaction data Protein expression data

27. Biomax Informatics AG Bioinformatics designed with you in mind. Topological clustering (SOM)

28. Biomax Informatics AG Bioinformatics designed with you in mind. Distribution of the genes

29. Biomax Informatics AG Bioinformatics designed with you in mind. Limitations Co-expression is no proof of functional association.  Integrate evidence from multiple sources.

30. Biomax Informatics AG Bioinformatics designed with you in mind. Integration with annotation Analyse gene expression data using integration with annotation catalogues. Functional catalogue Phenotypes Interaction

31. Biomax Informatics AG Bioinformatics designed with you in mind. Functional projection

32. Biomax Informatics AG Bioinformatics designed with you in mind. Looking at the gene lists

33. Biomax Informatics AG Bioinformatics designed with you in mind. FunCat Tool to structure information Tool to connect information

34. Biomax Informatics AG Bioinformatics designed with you in mind. Thank you!